| 1. |
- Potapov, Anton M., et al.
(författare)
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Global fine-resolution data on springtail abundance and community structure
- 2024
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.
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| 2. |
- Saxena, Richa, et al.
(författare)
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Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:2, s. 142-148
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Tidskriftsartikel (refereegranskat)abstract
- Glucose levels 2 h after an oral glucose challenge are a clinical measure of glucose tolerance used in the diagnosis of type 2 diabetes. We report a meta-analysis of nine genome-wide association studies (n = 15,234 nondiabetic individuals) and a follow-up of 29 independent loci (n = 6,958–30,620). We identify variants at the GIPR locus associated with 2-h glucose level (rs10423928, β (s.e.m.) = 0.09 (0.01) mmol/l per A allele, P = 2.0 × 10−15). The GIPR A-allele carriers also showed decreased insulin secretion (n = 22,492; insulinogenic index, P = 1.0 × 10−17; ratio of insulin to glucose area under the curve, P = 1.3 × 10−16) and diminished incretin effect (n = 804; P = 4.3 × 10−4). We also identified variants at ADCY5 (rs2877716, P = 4.2 × 10−16), VPS13C (rs17271305, P = 4.1 × 10−8), GCKR (rs1260326, P = 7.1 × 10−11) and TCF7L2 (rs7903146, P = 4.2 × 10−10) associated with 2-h glucose. Of the three newly implicated loci (GIPR, ADCY5 and VPS13C), only ADCY5 was found to be associated with type 2 diabetes in collaborating studies (n = 35,869 cases, 89,798 controls, OR = 1.12, 95% CI 1.09–1.15, P = 4.8 × 10−18).
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| 3. |
- Baudrier, Etienne, et al.
(författare)
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Retrieval of the ornaments from the Hand-Press Period : An overview
- 2009
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Ingår i: Proceedings of the International Conference on Document Analysis and Recognition, ICDAR. - : IEEE. - 9780769537252 ; , s. 496-500
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Konferensbidrag (refereegranskat)abstract
- This paper deals with the topic of the retrieval of document images focused on a specific application: the ornaments of the Hand-Press period. It presents an overview as a result of the work and the discussions undertaken by a workgroup on this subject. The paper starts by giving a general view about digital libraries of ornaments and associated retrieval problematics. Two main issues are underlined: content based image retrieval (CBIR) and image difference visualization. Several contributions are summarized, commented and compared. Conclusions and open problems arising from this overview are twofold: 1. contributions on CBIR miss scale-invariant methods and don't provide significative evaluation results. 2. robust registration is the open problem for visual comparison.
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| 4. |
- Chen, Hao Yu, et al.
(författare)
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Association of FADS1/2 Locus Variants and Polyunsaturated Fatty Acids With Aortic Stenosis
- 2020
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Ingår i: JAMA cardiology. - : American Medical Association (AMA). - 2380-6583 .- 2380-6591. ; 5:6, s. 694-702
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Tidskriftsartikel (refereegranskat)abstract
- Importance: Aortic stenosis (AS) has no approved medical treatment. Identifying etiological pathways for AS could identify pharmacological targets.Objective: To identify novel genetic loci and pathways associated with AS.Design, Setting, and Participants: This genome-wide association study used a case-control design to evaluate 44 703 participants (3469 cases of AS) of self-reported European ancestry from the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort (from January 1, 1996, to December 31, 2015). Replication was performed in 7 other cohorts totaling 256 926 participants (5926 cases of AS), with additional analyses performed in 6942 participants from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Follow-up biomarker analyses with aortic valve calcium (AVC) were also performed. Data were analyzed from May 1, 2017, to December 5, 2019.Exposures: Genetic variants (615 643 variants) and polyunsaturated fatty acids (ω-6 and ω-3) measured in blood samples.Main Outcomes and Measures: Aortic stenosis and aortic valve replacement defined by electronic health records, surgical records, or echocardiography and the presence of AVC measured by computed tomography.Results: The mean (SD) age of the 44 703 GERA participants was 69.7 (8.4) years, and 22 019 (49.3%) were men. The rs174547 variant at the FADS1/2 locus was associated with AS (odds ratio [OR] per C allele, 0.88; 95% CI, 0.83-0.93; P = 3.0 × 10-6), with genome-wide significance after meta-analysis with 7 replication cohorts totaling 312 118 individuals (9395 cases of AS) (OR, 0.91; 95% CI, 0.88-0.94; P = 2.5 × 10-8). A consistent association with AVC was also observed (OR, 0.91; 95% CI, 0.83-0.99; P = .03). A higher ratio of arachidonic acid to linoleic acid was associated with AVC (OR per SD of the natural logarithm, 1.19; 95% CI, 1.09-1.30; P = 6.6 × 10-5). In mendelian randomization, increased FADS1 liver expression and arachidonic acid were associated with AS (OR per unit of normalized expression, 1.31 [95% CI, 1.17-1.48; P = 7.4 × 10-6]; OR per 5-percentage point increase in arachidonic acid for AVC, 1.23 [95% CI, 1.01-1.49; P = .04]; OR per 5-percentage point increase in arachidonic acid for AS, 1.08 [95% CI, 1.04-1.13; P = 4.1 × 10-4]).Conclusions and Relevance: Variation at the FADS1/2 locus was associated with AS and AVC. Findings from biomarker measurements and mendelian randomization appear to link ω-6 fatty acid biosynthesis to AS, which may represent a therapeutic target.
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| 5. |
- Cormier, Bettie, 1993-, et al.
(författare)
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Chronic feeding exposure to virgin and spiked microplastics disrupts essential biological functions in teleost fish
- 2021
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Ingår i: Journal of Hazardous Materials. - : Elsevier. - 0304-3894 .- 1873-3336. ; 415
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Tidskriftsartikel (refereegranskat)abstract
- Toxicity of polyethylene (PE) and polyvinyl chloride (PVC) microplastics (MPs), either virgin or spiked with chemicals, was evaluated in two short-lived fish using a freshwater species, zebrafish, and a marine species, marine medaka. Exposures were performed through diet using environmentally relevant concentrations of MPs over 4 months. No modification of classical biomarkers, lipid peroxidation, genotoxicity or F0 behaviour was observed. A significant decrease in growth was reported after at least two months of exposure. This decrease was similar between species, independent from the type of MPs polymer and the presence or not of spiked chemicals, but was much stronger in females. The reproduction was evaluated and it revealed a significant decrease in the reproductive output for both species and in far more serious numbers in medaka. PVC appeared more reprotoxic than PE as were MPs spiked with PFOS and benzophenone-3 compared to MPs spiked with benzo[a]pyrene. Further, PVC-benzophenone-3 produced behavioural disruption in offspring larvae. These results obtained with two species representing different aquatic environments suggest that microplastics exert toxic effects, slightly different according to polymers and the presence or not of sorbed chemicals, which may lead in all cases to serious ecological disruptions.
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| 6. |
- Cormier, Bettie, et al.
(författare)
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Environmental microplastics disrupt swimming activity in acute exposure in Danio rerio larvae and reduce growth and reproduction success in chronic exposure in D. rerio and Oryzias melastigma
- 2022
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Ingår i: Environmental Pollution. - : Springer. - 0269-7491 .- 1873-6424. ; 308
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Tidskriftsartikel (refereegranskat)abstract
- Microplastics (MPs), widely present in aquatic ecosystems, can be ingested by numerous organisms, but their toxicity remains poorly understood. Toxicity of environmental MPs from 2 beaches located on the Guadeloupe archipelago, Marie Galante (MG) and Petit-Bourg (PB) located near the North Atlantic gyre, was evaluated. A first experiment consisted in exposing early life stages of zebrafish (Danio rerio) to MPs at 1 or 10 mg/L. The exposure of early life stages to particles in water induced no toxic effects except a decrease in larval swimming activity for both MPs exposures (MG or PB). Then, a second experiment was performed as a chronic feeding exposure over 4 months, using a freshwater fish species, zebrafish, and a marine fish species, marine medaka (Oryzias melastigma). Fish were fed with food supplemented with environmentally relevant concentrations (1% wet weight of MPs in food) of environmental MPs from both sites. Chronic feeding exposure led to growth alterations in both species exposed to either MG or PB MPs but were more pronounced in marine medaka. Ethoxyresorufin-O-deethylase (EROD) and acetylcholinesterase (AChE) activities were only altered for marine medaka. Reproductive outputs were modified following PB exposure with a 70 and 42% decrease for zebrafish and marine medaka, respectively. Offspring of both species (F1 generation) were reared to evaluate toxicity following parental exposure on unexposed larvae. For zebrafish offspring, it revealed premature mortality after parental MG exposure and parental PB exposure produced behavioural disruptions with hyperactivity of F1 unexposed larvae. This was not observed in marine medaka offspring. This study highlights the ecotoxicological consequences of short and long-term exposures to environmental microplastics relevant to coastal marine areas, which represent essential habitats for a wide range of aquatic organisms.
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| 7. |
- Hilton, Robert G., et al.
(författare)
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Erosion of organic carbon in the Arctic as a geological carbon dioxide sink
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 524:7563, s. 84-U162
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Tidskriftsartikel (refereegranskat)abstract
- Soils of the northern high latitudes store carbon over millennial timescales (thousands of years) and contain approximately double the carbon stock of the atmosphere(1-3). Warming and associated permafrost thaw can expose soil organic carbon and result in mineralization and carbon dioxide (CO2) release(4-6). However, some of this soil organic carbon may be eroded and transferred to rivers(7-9). If it escapes degradation during river transport and is buried in marine sediments, then it can contribute to a longer-term (more than ten thousand years), geological CO2 sink(8-10). Despite this recognition, the erosional flux and fate of particulate organic carbon (POC) in large rivers at high latitudes remains poorly constrained. Here, we quantify the source of POC in the Mackenzie River, the main sediment supplier to the Arctic Ocean(11,12), and assess its flux and fate. We combine measurements of radiocarbon, stable carbon isotopes and element ratios to correct for rock-derived POC10,13,14. Our samples reveal that the eroded biospheric POC has resided in the basin for millennia, with a mean radiocarbon age of 5,800 +/- 800 years, much older than the POC in large tropical rivers(13,14). From the measured biospheric POC content and variability in annual sediment yield(15), we calculate a biospheric POC flux of 2.2(-0.9)(+1.3) teragrams of carbon per year from the Mackenzie River, which is three times the CO2 drawdown by silicate weathering in this basin(16). Offshore, we find evidence for efficient terrestrial organic carbon burial over the Holocene period, suggesting that erosion of organic carbon-rich, high-latitude soils may result in an important geological CO2 sink.
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| 8. |
- Lang, Daniel, et al.
(författare)
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The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
- 2018
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Ingår i: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 93:3, s. 515-533
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Tidskriftsartikel (refereegranskat)abstract
- The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene-and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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| 9. |
- Lihoreau, Mathieu, et al.
(författare)
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Collective selection of food patches in Drosophila
- 2016
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Ingår i: Journal of Experimental Biology. - : The Company of Biologists. - 0022-0949 .- 1477-9145. ; 219:5, s. 668-675
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Tidskriftsartikel (refereegranskat)abstract
- The fruit fly Drosophila melanogaster has emerged as a model organism for research on social interactions. Although recent studies have described how individuals interact on foods for nutrition and reproduction, the complex dynamics by which groups initially develop and disperse have received little attention. Here we investigated the dynamics of collective foraging decisions by D. melanogaster and their variation with group size and composition. Groups of adults and larvae facing a choice between two identical, nutritionally balanced food patches distributed themselves asymmetrically, thereby exploiting one patch more than the other. The speed of the collective decisions increased with group size, as a result of flies joining foods faster. However, smaller groups exhibited more pronounced distribution asymmetries than larger ones. Using computer simulations, we show how these non-linear phenomena can emerge from social attraction towards occupied food patches, whose effects add up or compete depending on group size. Our results open new opportunities for exploring complex dynamics of nutrient selection in simple and genetically tractable groups.
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| 10. |
- Peel, Jessica N., et al.
(författare)
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Neutralizing IFN-γ autoantibodies are rare and pathogenic in HLA-DRB1*15:02 or 16:02 individuals
- 2024
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Ingår i: Journal of Clinical Investigation. - : American Society For Clinical Investigation. - 0021-9738 .- 1558-8238. ; 134:8
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND. Weakly virulent environmental mycobacteria (EM) can cause severe disease in HLA-DRB1*15:02 or 16:02 adults harboring neutralizing anti-IFN-γ autoantibodies (nAIGAs). The overall prevalence of nAIGAs in the general population is unknown, as are the penetrance of nAIGAs in HLA-DRB1*15:02 or 16:02 individuals and the proportion of patients with unexplained, adult-onset EM infections carrying nAIGAs.METHODS. This study analyzed the detection and neutralization of anti-IFN-γ autoantibodies (auto-Abs) from 8,430 healthy individuals of the general population, 257 HLA-DRB1*15:02 or 16:02 carriers, 1,063 patients with autoimmune disease, and 497 patients with unexplained severe disease due to EM.RESULTS. We found that anti-IFN-γ auto-Abs detected in 4,148 of 8,430 healthy individuals (49.2%) from the general population of an unknown HLA-DRB1 genotype were not neutralizing. Moreover, we did not find nAIGAs in 257 individuals carrying HLA-DRB1* 15:02 or 16:02. Additionally, nAIGAs were absent in 1,063 patients with an autoimmune disease. Finally, 7 of 497 patients (1.4%) with unexplained severe disease due to EM harbored nAIGAs.CONCLUSION. These findings suggest that nAIGAs are isolated and that their penetrance in HLA-DRB1*15:02 or 16:02 individuals is low, implying that they may be triggered by rare germline or somatic variants. In contrast, the risk of mycobacterial disease in patients with nAIGAs is high, confirming that these nAIGAs are the cause of EM disease.
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